LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-584-g3e8807bee0-modified)
  using 1 OpenMP thread(s) per MPI task
# created by fftool

units real
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls

special_bonds lj/coul 0.0 0.0 0.5

pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0 coul/tt 4 8.0
pair_modify tail yes
kspace_style pppm 1.0e-5

read_data data.ethylene_glycol
Reading data file ...
  orthogonal box = (0 0 0) to (35 35 35)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  2800 atoms
  scanning bonds ...
  2 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  9 = max dihedrals/atom
  orthogonal box = (0 0 0) to (35 35 35)
  1 by 1 by 1 MPI processor grid
  reading bonds ...
  2600 bonds
  reading angles ...
  2800 angles
  reading dihedrals ...
  3000 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0.5     
  special bond factors coul:  0        0        0.5     
     5 = max # of 1-2 neighbors
     6 = max # of 1-3 neighbors
    10 = max # of 1-4 neighbors
    13 = max # of special neighbors
  special bonds CPU = 0.001 seconds
  read_data CPU = 0.019 seconds

pair_coeff    1    1 lj/cut/coul/long     0.057289     3.500000  # CTO CTO ~
pair_coeff    1    2 lj/cut/coul/long     0.091945     3.304542  # CTO OHG ~
pair_coeff    1    3 lj/cut/coul/long     0.038625     2.958040  # CTO H1O ~
pair_coeff    1    4 lj/cut/coul/long     0.000000     0.000000  # CTO HOG ~
pair_coeff    2    2 lj/cut/coul/long     0.147565     3.120000  # OHG OHG ~
pair_coeff    2    3 lj/cut/coul/long     0.061990     2.792848  # OHG H1O ~
pair_coeff    2    4 lj/cut/coul/long     0.000000     0.000000  # OHG HOG ~
pair_coeff    3    3 lj/cut/coul/long     0.026041     2.500000  # H1O H1O ~
pair_coeff    3    4 lj/cut/coul/long     0.000000     0.000000  # H1O HOG ~
pair_coeff    4    4 lj/cut/coul/long     0.000000     0.000000  # HOG HOG ~
pair_coeff    *   5* lj/cut/coul/long     0.000000     0.000000
pair_coeff    1    1 thole   1.662
pair_coeff    1    2 thole   1.561
pair_coeff    1    5 thole   1.662
pair_coeff    1    6 thole   1.561
pair_coeff    2    2 thole   1.467
pair_coeff    2    5 thole   1.561
pair_coeff    2    6 thole   1.467
pair_coeff    5    5 thole   1.662
pair_coeff    5    6 thole   1.561
pair_coeff    6    6 thole   1.467
pair_coeff    2    4 coul/tt  4.5 1.0
pair_coeff    4    6 coul/tt  4.5 1.0
pair_coeff    1    4 coul/tt  4.5 1.0
pair_coeff    4    5 coul/tt  4.5 1.0

group ATOMS type 1 2 3 4
2000 atoms in group ATOMS
group CORES type 1 2
800 atoms in group CORES
group DRUDES type 5 6
800 atoms in group DRUDES

fix DRUDE all drude C C N N D D

fix SHAKE ATOMS shake 0.0001 20 0 b 3 4
Finding SHAKE clusters ...
     400 = # of size 2 clusters
     400 = # of size 3 clusters
       0 = # of size 4 clusters
       0 = # of frozen angles
  find clusters CPU = 0.000 seconds

neighbor 2.0 bin

timestep 1.0

variable TK equal 298.0
variable TDK equal 1.0
variable PBAR equal 1.0

comm_modify vel yes
velocity ATOMS create ${TK} 12345
velocity ATOMS create 298 12345

compute TATOM ATOMS temp
compute TDRUDE all temp/drude

fix DTDIR all drude/transform/direct
fix TSTAT ATOMS npt temp ${TK} ${TK} 200 iso ${PBAR} ${PBAR} 1000
fix TSTAT ATOMS npt temp 298 ${TK} 200 iso ${PBAR} ${PBAR} 1000
fix TSTAT ATOMS npt temp 298 298 200 iso ${PBAR} ${PBAR} 1000
fix TSTAT ATOMS npt temp 298 298 200 iso 1 ${PBAR} 1000
fix TSTAT ATOMS npt temp 298 298 200 iso 1 1 1000
fix_modify TSTAT temp TATOM press thermo_press
WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1402)
fix TSTDR DRUDES nvt temp ${TDK} ${TDK} 50
fix TSTDR DRUDES nvt temp 1 ${TDK} 50
fix TSTDR DRUDES nvt temp 1 1 50
fix DTINV all drude/transform/inverse

fix ICECUBE all momentum 1000 linear 1 1 1

thermo_style custom step etotal ke pe ebond eangle evdwl ecoul elong   press vol density c_TATOM c_TDRUDE[1] c_TDRUDE[2]
thermo 50

run 500
PPPM initialization ...
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.41206781
  grid = 54 54 54
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0040479865
  estimated relative force accuracy = 1.2190391e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 250047 157464
Generated 0 of 15 mixed pair_coeff terms from geometric mixing rule
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 13
New max number of 1-2 to 1-4 neighbors: 13 (+0)
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10
  ghost atom cutoff = 10
  binsize = 5, bins = 7 7 7
  3 neighbor lists, perpetual/occasional/extra = 3 0 0
  (1) pair lj/cut/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
  (2) pair thole, perpetual, skip from (1)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (3) pair coul/tt, perpetual, skip from (1)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 39.43 | 39.43 | 39.43 Mbytes
   Step         TotEng         KinEng         PotEng         E_bond        E_angle         E_vdwl         E_coul         E_long         Press          Volume        Density        c_TATOM      c_TDRUDE[1]    c_TDRUDE[2]  
         0   2707.9279      1420.362       1287.5659      1474.8647      30.734202     -461.31379      540022.21     -539778.93     -9408.4249      42875          0.48077588     298            294.34401      6.9394757    
        50   1418.467       1249.502       168.96497      309.99547      480.01553     -495.04808      539716.53     -540017.02      3344.2842      42776.949      0.48187789     252.07241      255.56807      12.841401    
       100   1391.631       1287.2692      104.36186      333.86639      427.43216     -456.38002      539638.17     -540023.61     -3962.1778      42668.283      0.48310512     265.74273      268.23371      3.3477455    
       150   1404.7856      1334.1949      70.590683      285.69317      480.49155     -340.69069      539518.01     -540045.75     -2082.9179      42395.713      0.48621109     274.19439      278.94631      1.6008218    
       200   1425.8195      1378.4983      47.321171      460.3582       459.3409      -415.44784      539411.67     -540044.6       6205.8019      42117.045      0.48942811     284.32249      288.46228      1.1474819    
       250   1451.5309      1408.0792      43.451738      376.36323      598.22562     -302.55742      539235.03     -540053.8      -3523.5218      41843.302      0.49263001     290.29736      294.90586      0.66500712   
       300   1460.332       1532.4503     -72.118254      394.6394       561.19471     -334.56111      539192.83     -540050.12      4984.7166      41569.485      0.49587494     316.03916      320.88626      0.85911371   
       350   1465.3212      1564.1495     -98.828268      418.43274      585.9734      -296.62446      539077.24     -540036.78      740.63503      41386.894      0.49806264     322.55702      327.69189      0.54088861   
       400   1446.0616      1528.7734     -82.711822      414.46911      582.4179      -279.8947       539064.81     -540045.35     -1758.1168      41241.935      0.49981326     314.95183      320.11174      0.86626688   
       450   1411.6634      1569.3079     -157.64449      380.53381      668.13738     -290.80868      538968.35     -540032.62      3122.7516      41154.154      0.50087936     323.37847      328.4585       1.1708531    
       500   1366.0204      1653.5925     -287.57202      433.2513       598.39315     -281.96478      538837.41     -540025.77     -2921.4645      41080.822      0.50177345     340.52409      346.02903      1.3744493    
Loop time of 12.3334 on 1 procs for 500 steps with 2800 atoms

Performance: 3.503 ns/day, 6.852 hours/ns, 40.540 timesteps/s, 113.513 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 3.1504     | 3.1504     | 3.1504     |   0.0 | 25.54
Bond    | 0.23813    | 0.23813    | 0.23813    |   0.0 |  1.93
Kspace  | 4.0929     | 4.0929     | 4.0929     |   0.0 | 33.19
Neigh   | 0.23938    | 0.23938    | 0.23938    |   0.0 |  1.94
Comm    | 0.022135   | 0.022135   | 0.022135   |   0.0 |  0.18
Output  | 0.00054188 | 0.00054188 | 0.00054188 |   0.0 |  0.00
Modify  | 4.5843     | 4.5843     | 4.5843     |   0.0 | 37.17
Other   |            | 0.005628   |            |       |  0.05

Nlocal:           2800 ave        2800 max        2800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           6816 ave        6816 max        6816 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         446968 ave      446968 max      446968 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 446968
Ave neighs/atom = 159.63143
Ave special neighs/atom = 11.714286
Neighbor list builds = 28
Dangerous builds = 0

Total wall time: 0:00:12
